KABUL, Afghanistan — Afghanistan’s presidential election was cast into crisis on Wednesday as the candidate Abdullah Abdullah announced a boycott of the electoral process, accusing his opponent and President Hamid Karzai of engineering huge fraud in the runoff vote on Saturday.

Rejecting the process laid out under Afghan electoral law, he called on the election commission to halt all vote-counting and immediately investigate any inflated ballot totals — steps that are designed to come after partial vote results are announced in the next few weeks. Mr. Abdullah also withdrew his election observers from the vote-counting and suspended his cooperation with the Independent Election Commission, which his campaign accuses of bias.

“We are asking for the counting process to be stopped immediately because this is not a legitimate process,” he said. “The fraud was engineering in such an exceptional way that it left no choice for us but to make this announcement today and wait for the response and correction of this.”

If Mr. Abdullah were to reject the official results of the vote, it would cast into doubt an election that Western and Afghan officials alike have considered critical to the legacy of the long Western war in Afghanistan. The election’s legitimacy has been directly tied to the country’s stability, and to continued international aid now that Western troops are leaving.

Mr. Abdullah is complaining that as many as two million of the seven million votes initially estimated to have been cast Saturday are the result of methodical ballot-box stuffing, mostly in favor of his rival, Ashraf Ghani. He also claims that at least one senior member of the Independent Election Commission has been involved in trying to rig the election for Mr. Ghani.

But no official numbers at all have been released yet by the election commission, and Mr. Abdullah is trying to press his case before the official fraud adjudication phase.

In a bluntly worded statement, the United Nations called for the candidates to respect the national electoral system they both vowed to abide by when opening their campaigns. “We believe that the electoral process should continue as laid out in the laws passed by the National Assembly,” said Jan Kubis, the special representative for the secretary general for Afghanistan.

“Our team considers this unexpected decision a violation of the contract signed between the candidates and the I.E.C.,” said Faizullah Zaki, a spokesman for Mr. Ghani’s campaign.

President Karzai’s office has also rejected the fraud accusations made by Mr. Abdullah’s campaign, and suggested that the president was trying to act as a peacemaker between the candidates on Wednesday. “The president respects both candidates, and he has been in touch with both of them,” said Adela Raz, a presidential spokeswoman. “He does believe both candidates respect each other and want prosperity for Afghanistan.”

By stepping outside the legal election system, Mr. Abdullah is taking up a double-edged sword. While he may succeed in winning more scrutiny of election officials’ neutrality, he also risks undermining the very process by which he hopes to be elected, and drawing accusations that he might be boycotting the election simply because he fears he might lose.

And in a country with a violent history of factional divisions, some here worry that even more is at risk if an election deadlock stretches on.

Mr. Abdullah has picked up important endorsements by some nationally prominent politicians from the country’s ethnic Pashtun majority, suggesting that he had expanded his support base since he opposed Mr. Karzai in the 2009 presidential election. But his support has remained the strongest among Afghanistan’s ethnic Tajik minority, and in particular among powerful warlords and power brokers who joined together in the Northern Alliance against the Taliban in 2001.

Even before the voting began in April, some of those supporters said they thought it was clear that Mr. Abdullah would win, and suggested that he would lose only as a result of conspiracy.

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Abdullah Abdullah, a candidate for Afghanistan’s presidency, said he suspended work with the country’s electoral bodies and asked officials to stop counting votes because of widespread fraud.CreditCreditShah Marai/Agence France-Presse — Getty Images

The depth of those emotions and the civil war-era factional divisions they are rooted in have some here concerned about the potential for violence. Those worries intensified Wednesday night after the followers of two powerful former warlords on opposite sides of the campaign clashed on the outskirts of Kabul. At least one person was killed in the clash, according to the Afghan Interior Ministry.

Mr. Abdullah’s protest is rooted in distrust of the election commission authorized by Mr. Karzai, officials say. His campaign has called on the election commission to suspend one of its high-ranking officials, Ziaulhaq Amarkhel, who has been accused of transporting a truckload of blank ballots under suspicious circumstances. Mr. Amarkhel denies the accusations.

“Dr. Abdullah has come to a point where he believes he is in the race against four other contenders” — Mr. Ghani, the election commission, the complaints commission and the government, said Wahid Omar, a senior adviser to Mr. Abdullah. “None of these bodies is actually impartial in the process.”

The campaign has also demanded an investigation of whether ballot totals were fraudulently inflated in the runoff. His aides released numbers for some eastern provinces, where Mr. Ghani is likely to have strong support from ethnic Pashtun voters, suggesting that the number of votes cast in those regions far outstripped the plausible number of registered voters.

One of those was Khost Province, an insecure region where the Taliban insurgency is strong. Provincial election officials reported that turnout there was roughly three times higher than it was in the first round, with more than 400,000 voters casting ballots, according to the early estimates provided by provincial election officials. But the estimated population of the entire province, according to the country’s central statistics office, is less than 550,000, including children.

Officials at the Kabul headquarters of Afghanistan’s Independent Election Commission, which oversees the voting and tallying, would not comment on the numbers being offered by provincial officials.

One senior Afghan security official, speaking on the condition of anonymity, said that he suspected there had been “ample amounts” of fraud. But he emphasized that there was no hard evidence yet, and he could not confirm the numbers offered by provincial election officials.

The official said that in contrast to the April vote, it appeared that this time the fraud was not so evenly spread among the candidates. He said officials suspected that Mr. Ghani benefited more this time based on a large rise in voter turnout in provinces that supported him in April. But at least some of that increase may have been authentic, he said — a reflection of ethnic Pashtun voters rallying their support behind Mr. Ghani now that the election field had narrowed.

It was unclear on Wednesday what Mr. Abdullah would do if the election commission did not meet his demands.

Campaign officials for Mr. Abdullah said they were not, for now, calling for a new vote. In a news conference, Mr. Abdullah said that one answer might be the creation of a joint commission including representatives from both campaigns and overseen by the United Nations. The chances of that, however, seemed to diminish after the United Nations’ statement later in the evening.

Mr. Abdullah’s fraud accusations against Mr. Karzai in the 2009 vote threw that election into crisis. International officials stepped in to force a runoff vote, but Mr. Abdullah withdrew from the process under protest, and Mr. Karzai was declared the winner.

Mr. Abdullah has insisted that he will not stand for such a result this time. And the question about what his supporters will do now hangs over the process.

In the Panjshir Valley, the heartland of the old Northern Alliance in which Mr. Abdullah first rose to prominence, the allegations of fraud seemed by Wednesday to have become taken as established fact.

“Dr. Abdullah is the rightful president of Afghanistan,” said Mubin Rahman, 25, a security official in Bazarak, the capital of Panjshir.

He and many interviewed in Panjshir on Wednesday predicted widespread protests if Mr. Abdullah was not declared the winner.

Mr. Rahman insisted that Afghans of all ethnicities and political loyalties wanted peace above all else. “But if there is no other choice,” he added, “there may be violent resistance.”

A version of this article appears in print on , Section A, Page 8 of the New York edition with the headline: Candidate’s Protest Clouds Afghan Vote-Counting for President. Order Reprints | Today’s Paper | Subscribe